def buildList(self, coords): # neib_list = np.reshape(self.neib_list, -1) self.buildcount += 1 if self.onelist: # nlist = _fortran_utils.build_neighbor_list1( # coords, self.Alist, neib_list, self.rlist2) if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list1_periodic( coords, self.Alist, self.nlistmax * 2, self.rlist2, self.boxl ) else: neib_list, nlist = _fortran_utils.build_neighbor_list1( coords, self.Alist, self.nlistmax * 2, self.rlist2 ) else: if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list2_periodic( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2, self.boxl ) else: neib_list, nlist = _fortran_utils.build_neighbor_list2( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2 ) neib_list = np.reshape(neib_list, [-1, 2]) return neib_list[:nlist, :]
def buildList(self, coords): # neib_list = np.reshape(self.neib_list, -1) self.buildcount += 1 self.oldcoords = np.copy(np.reshape(coords, [-1, 3])) # raw_input("press enter to continue: onelist %d, len(alist)=%d, len(coords)=%d" % (self.onelist, len(self.Alist), len(coords))) if self.onelist: # nlist = _fortran_utils.build_neighbor_list1( # coords, self.Alist, neib_list, self.rlist2) if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list1_periodic( coords, self.Alist, self.nlistmax * 2, self.rlist2, self.boxl ) else: neib_list, nlist = _fortran_utils.build_neighbor_list1( coords, self.Alist, self.nlistmax * 2, self.rlist2 ) else: if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list2_periodic( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2, self.boxl ) else: neib_list, nlist = _fortran_utils.build_neighbor_list2( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2 ) self.neib_list = np.reshape(neib_list, [-1, 2]) self.nlist = nlist
def buildList(self, coords): #neib_list = np.reshape(self.neib_list, -1) self.buildcount += 1 self.oldcoords = np.copy(np.reshape(coords, [-1, 3])) # raw_input("press enter to continue: onelist %d, len(alist)=%d, len(coords)=%d" % (self.onelist, len(self.Alist), len(coords))) if self.onelist: #nlist = _fortran_utils.build_neighbor_list1( # coords, self.Alist, neib_list, self.rlist2) if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list1_periodic( coords, self.Alist, self.nlistmax * 2, self.rlist2, self.boxl) else: neib_list, nlist = _fortran_utils.build_neighbor_list1( coords, self.Alist, self.nlistmax * 2, self.rlist2) else: if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list2_periodic( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2, self.boxl) else: neib_list, nlist = _fortran_utils.build_neighbor_list2( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2) self.neib_list = np.reshape(neib_list, [-1, 2]) self.nlist = nlist
def buildList(self, coords): #neib_list = np.reshape(self.neib_list, -1) self.buildcount += 1 if self.onelist: #nlist = _fortran_utils.build_neighbor_list1( # coords, self.Alist, neib_list, self.rlist2) if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list1_periodic( coords, self.Alist, self.nlistmax * 2, self.rlist2, self.boxl) else: neib_list, nlist = _fortran_utils.build_neighbor_list1( coords, self.Alist, self.nlistmax * 2, self.rlist2) else: if self.periodic: neib_list, nlist = _fortran_utils.build_neighbor_list2_periodic( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2, self.boxl) else: neib_list, nlist = _fortran_utils.build_neighbor_list2( coords, self.Alist, self.Blist, self.nlistmax * 2, self.rlist2) neib_list = np.reshape(neib_list, [-1, 2]) return neib_list[:nlist, :]